Ok first to the idea of remapping the command/control keys. Not a good idea. Those switching are or atleast should expect some relearning to be involved with the switch. Remapping the keys would only serve to antagonize the very loyal current Mac Base.
To the point about a multiple button mouse. This is not a feature that is missing from the OS and that is what this article is about. The OS does support a multiple button mouse, Apple have simply chosen to ship a single button mouse. To AngryHamster's comments as to wether a single or multiple button mouse is more ore less complex, for the most part that is subjective as eitehr can be learned equally easily. You state that you do tech support and the in your opinion less than have your user base currently uses the right mouse button. Assuming recent numbers are accurate as is your estimation. Estimations are that 400,000 windows users have switched to the Mac over the last 2 quarters. Assuming your estimation of less than half of your users using the right mouse button that would mean 200,000 right clicking users have switched to Macintosh in the last 2 quarters. A rather sizeable number, and while there are no numbers that I am aware of indicating those switching the other direction, I would venture a guess that the flow is greater towards the Mac rather than away from. Seems to me the lack of an included piece of hardware has not swayed users from the platform. Also, I will venture a guess (somewhat educated as I as well do support for a mixed environment) that well more than half of all Mac users are control clicking. Now to just breifly touch on my thought of which is more complex, let's take a support call from a windows user and a mac user. In both cases we will tell the user to click on a particular item. How often from the other end when speaking to the windows user have you heard them ask "Left or right click?" How often have you heard the Mac user ask "Do you mean control click?" I'll bet my next check against yours that you've heard the windows response far more often. Now tell me which is more confusiing? Bottom line if you feel more productive with a multiple button mouse get one and plug it in.
Save buttons in the toolbars. Well some might find this a nice feature and some may not, but as with the multiple button mouse topic, this is not an OS level item. It is not the Windows OS that provides the Save button but the application developers. You want them beat on them. I'm always up for having options.
Sorting folders to the top of a list. Can we take this one step further? I'd like to be able to sort an open or save dialog list in any order that I like, by name, date, kind.
More contextual help. YES! Any additional readily available help is a plus.
What OS X Could Learn From Windows